There are a number of assays and sensors for the detection of the presence and/or concentration of specific substances in fluids and gases. Many of these rely on specific ligand/antiligand reactions as the mechanism of detection. That is, pairs of substances (i.e. the binding pairs or ligand/antiligands) are known to bind to each other, while binding little or not at all to other substances. This has been the focus of a number of techniques that utilize these binding pairs for the detection of the complexes. These generally are done by labeling one component of the complex in some way, so as to make the entire complex detectable, using, for example, radioisotopes, fluorescent and other optically active molecules, enzymes, etc.
Advances in technology have provided techniques for assaying multiple analytes (“multiplexing”) at the same time. Assaying of multiple analytes created a need for development of improved methods of sample and data analysis in which information about identity of each analyte is retained.
Examples of where multiplexing assays for DNA and proteins have been utilized include those for cytokines (e.g. U.S. Pat. No. 6,649,351), phosphoproteins (Pelech (2004); Curr. Pharm. Biotechnol. 5, 69-77), and single nucleotide polymorphisms (SNPs).
SNP genotyping using MALDI-TOF mass spectrometry is discussed by Pusch et al. (2002), Pharmacogenomics 3, 537-548. Most SNP assays involve identifying differences in polymorphisms by discriminating between the mass of individual nucleotides (Griffin et al. (2000), Analytical Chemistry 72, 3298-3302; Griffin et al. (2000), TIBTECH, 18, 77-84) or by using a mass/charge tag system (Sauer et al. (2000), Nucleic Acid Research 28, e100).
Mass spectroscopy has found applications in combinatorial chemistry as discussed, for example, by Triolo (Triolo et al. (2001), Journal of Mass Spectroscopy 36, 1249-1259). Analytical construct technology has been successfully applied to the single-bead analysis of a split-mix combinatorial library, using an analytical fragment highly sensitized to electrospray mass spectrometry (ESI-MS) and easily identified by isotope labeling (Lorthioir et al. (2001), Analytical Chemistry 73, 963-970). Spatially-resolved time-of-flight mass spectroscopy has also been discussed (Winograd et al. (2001), Spectroscopy 16, 14-27).
U.S. Pat. No. 6,649,414 provides a fluorescent particle including a core or carrier particle having on its surface a plurality of smaller polymeric particles or nanoparticles, which are stained with different fluorescent dyes. When excited by a light source they are capable of giving off multiple fluorescent emissions simultaneously, which is useful for multiplexed analysis of a plurality of analytes in a sample.
U.S. Pat. No. 6,680,211 provides a fluorescent microsphere comprised of a plurality of fluorescent nanocrystals embedded in a polymeric microsphere.
U.S. Pat. No. 6,387,623 provides materials and methods for identifying chemical compounds having desired binding properties towards a binding partner of pharmaceutical interest. The method employs transponders associated with the solid phase material used in the assay and a scanner to encode and decode data stored electronically on the transponder.
U.S. Pat. No. 6,858,394 relates to sensor compositions comprising a composite array of individual arrays, to allow for simultaneous processing of a number of samples.
U.S. Pat. No. 6,824,981 discloses compositions and methods for sensitive detection of one or multiple analytes. In general, the methods involve the use of special label components, referred to as reporter signals, that can be associated with, incorporated into, or otherwise linked to the analytes.
U.S. Pat. No. 6,607,878 is directed to methods and kits for creating and analyzing molecules using uniquely identifiable tags. The invention is also directed to methods and kits that use uniquely identifiable tags for sequencing DNA, for determining mutations, including substitutions, deletions, and additions, in sample genes, and monitoring mRNA populations.
U.S. Pat. No. 6,340,588 provides combinations, called matrices with memories, of matrix materials that are encoded with an optically readable code. The matrix materials are those that are used as supports in solid phase chemical and biochemical syntheses, immunoassays and hybridization reactions. The matrix materials may additionally include fluorophores or other luminescent moieties to produce luminescing matrices with memories. The memories include electronic and optical storage media and also include optical memories, such as bar codes and other machine-readable codes.
U.S. Pat. No. 6,649,351 provides a method for detecting a target analyte, by: (a) contacting one or more target analytes with a set of first and second binding reagents under conditions sufficient for binding of a target analyte with the first and second binding reagents, each of the first binding reagents containing a cleavage-inducing moiety and a target binding moiety, each of the second binding reagents containing a tagged probe having a mass modifier region attached to a target binding moiety by a cleavable linkage, the cleavable linkage being susceptible to cleavage when in proximity to an activated cleavage-inducing moiety; (b) activating the cleavage-inducing moiety to release a tag reporter, and (c) detecting a mass of the tag reporter, the mass uniquely corresponding to a known target analyte.
Multiplexing assays can be performed in numerous ways, however, most optimal analyte detection formats previously available limited the number of multiplexed assays that can be performed from a few in most cases to perhaps 50-100 in the best cases.